The gallery actually does maintain a “total download count” across all versions of a module (w/ same package ID) in the gallery, but it’s not displaying it right now. You can only see it in the feed:
So if you do delete an older version of a module on the gallery, it will affect this total count. One “manual workaround” I have been offering to folks is to send me email (or just contact
firstname.lastname@example.org) after uploading your new module version, and I can manually set the total downloads for that new version to match the download count for the previous version (and then it will
continue to increment as the new version is downloaded). I can then delete the old version from the gallery on your behalf.
Once we start the next wave of feature work for the gallery (very soon, I promise!), we’ll fix this properly to display the aggregate download count across all versions, and to collapse all versions under a single
details page for the module (displaying the individual download counts for each version too).
Hope this helps. Let me know if you want me to apply that workaround for you in the meantime.